{
  "checker": {
    "claims": [
      {
        "claim": "Each server can maintain multiple isolated modelling sessions; a MaBoSS session is created and its label is returned",
        "command": "<guest-path> tools/call {\"tool\": \"create_session\", \"arguments\": {\"label\": \"coldpass-claim-5521\"}}",
        "evidence": "\u2026coldpass-claim-5521) (set as default)\", \"type\": \"text\"}], \"isError\": false, \"structuredContent\": {\"result\": \"Session created: 36fd9abe-31c8-44f2-9447-3f8f4c514711 (coldpass-claim-5521) (set as default)\"}}",
        "expected": "session created with that label returned",
        "input": "{\"tool\": \"create_session\", \"arguments\": {\"label\": \"coldpass-claim-5521\"}}",
        "kind": "claim",
        "outcome": "Real input produced the expected result: coldpass-claim-5521",
        "source": "Each server can maintain multiple isolated modelling sessions.",
        "source_checked": true,
        "source_file": "README.md",
        "verdict": "yes"
      }
    ],
    "cycle_checks": [
      {
        "claim": "Scheduled or looping main behavior",
        "command": "",
        "evidence": "Inspected README.md (Installation, Configure an MCP client, Sessions/artifacts, Run from source) and the four console entry points (mcp-neko-server, mcp-maboss-server, mcp-physicell-server, mcp-biomass-server). They serve MCP over stdio and expose no cron, loop, webhook, --once or --now trigger. The only CI schedule is in .github/workflows, which is not a product cycle.",
        "expected": "identify the product trigger",
        "input": "source inspection",
        "kind": "cycle",
        "outcome": "Inspected README.md (Installation, Configure an MCP client, Sessions/artifacts, Run from source) and the four console entry points (mcp-neko-server, mcp-maboss-server, mcp-physicell-server, mcp-biomass-server). They serve MCP over stdio and expose no cron, loop, webhook, --once or --now trigger. The only CI schedule is in .github/workflows, which is not a product cycle.",
        "source": "repository entry points",
        "verdict": "yes"
      }
    ],
    "details": {
      "argv": [
        "<guest-path>"
      ],
      "kind": "mcp",
      "scope": "product operation",
      "serverInfo": {
        "description": "Configure, simulate, analyze, and visualize Boolean models with MaBoSS.",
        "name": "MaBoSS",
        "title": "MaBoSS Boolean Model Simulator",
        "version": "2.5.2"
      },
      "tool_result": {
        "content": [
          {
            "text": "Session created: 77e20301-ee04-46ac-9beb-e8030b8dfc77 (coldpass-probe-7319) (set as default)",
            "type": "text"
          }
        ],
        "isError": false,
        "structuredContent": {
          "result": "Session created: 77e20301-ee04-46ac-9beb-e8030b8dfc77 (coldpass-probe-7319) (set as default)"
        }
      },
      "tool_result_checked": true,
      "tool_schema_bytes": 74564,
      "tools": [
        "edit_maboss_readouts",
        "export_handoff_bundle",
        "create_session",
        "list_sessions",
        "list_artifact_sessions",
        "set_default_session",
        "delete_session",
        "import_neko_handoff",
        "bnet_to_bnd_and_cfg",
        "build_simulation",
        "run_simulation",
        "export_maboss_bnd_cfg",
        "export_maboss_handoff",
        "get_maboss_nodes",
        "get_maboss_initial_state",
        "get_maboss_logical_rules",
        "change_maboss_rule",
        "get_maboss_mutations",
        "update_maboss_parameters",
        "set_maboss_output_nodes",
        "set_maboss_initial_state",
        "simulate_mutation",
        "visualize_network_trajectories",
        "get_simulation_result",
        "list_generated_files",
        "clean_generated_files"
      ],
      "working": true
    },
    "evidence_strength": "readme_checked",
    "example_checks": [],
    "status": "PASS"
  },
  "deviations": [
    "Preflight path /inputs/coldpass-preflight.py does not exist in this VM; used <guest-path> as instructed by the checker path.",
    "First installed the PyPI release of 2.5.2, then reinstalled from the workspace source as README 'Run from source' describes; both report version 2.5.2 and the final replay used the source build.",
    "Workspace has no .git metadata; the pinned git fetch/reset was not performed because the source was already present and no git operation was needed to run the product. The pinned commit d9079ee2eb8965d27939631da98117abe774091b could not be verified in the guest.",
    "README documents no test command or example invocation beyond --help/--version, so examples.json is empty; the repo's offline pytest suite was not run as product evidence.",
    "Cycles: no cron, loop, webhook, --once or --now behavior in the product, so detected=false."
  ],
  "fault_owner": null,
  "main_blocker": null,
  "operation": "Install mcp-biomodelling-servers from the source checkout and drive the MaBoSS MCP server over stdio: call create_session with a label and read the returned session ID and label.",
  "operation_scope": "Linux guest, Python 3.12.3 venv at <guest-path> (README requires Python 3.10-3.15). Covers the MaBoSS server only; NeKo, PhysiCell and BioMASS entry points were installed and report version 2.5.2 but were not exercised. No browser needed; CDP endpoint http://<internal-ip>:9226/json/version returned HTTP 200 (Chrome/155.0.8059.84) but no browser operation was run.",
  "outcome": "working",
  "plain_failure": null,
  "steps": [
    "python3 -m venv <guest-path>",
    "<guest-path> -m pip install --upgrade pip",
    "<guest-path> -m pip install mcp-biomodelling-servers (initial install, then replaced)",
    "<guest-path> -m pip install --force-reinstall --no-deps . (run from <guest-path>, README 'Run from source')",
    "<guest-path> --version -> mcp-maboss-server (mcp-biomodelling-servers) 2.5.2",
    "MCP tools/call create_session {\"label\":\"coldpass-probe-7319\"} via <guest-path> -> 'Session created: <uuid> (coldpass-probe-7319) (set as default)'",
    "<env-var>=<guest-path> python3 -I <guest-path> --validate --replay -> valid true, replay PASS"
  ],
  "stuck_step": null,
  "suggested_fix": "None required for the exercised MaBoSS path. Optionally add a documented example command to the README so examples can be replayed."
}